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Cookiecutter specifications


Unique identifier OMICS_09649
Name Cookiecutter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Cookiecutter takes as input one or several FASTQ files or one or several pairs of FASTQ files and requires a file with a list of k-mers for filtering.
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Make, gcc, Python
Maintained Yes


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  • person_outline Aleksey Komissarov <>

Publication for Cookiecutter

Cookiecutter in publications

PMCID: 5924527
PMID: 29597328
DOI: 10.3390/genes9040185

[…] libraries and sequencing were performed following lee et al []., filtration of the pe library lib400 was performed in two stages. first, reads containing long adapter fragments were removed using cookiecutter []. then trimmomatic [] was used to filter out reads with short adapter fragments. however, according to the discovar requirements no trimming or quality filtration was performed […]

PMCID: 5634325
PMID: 28994825
DOI: 10.1038/sdata.2017.151

[…] visualizations within shareable jupyter notebooks. the clustergrammer-widget utilizes the core clustergrammer-js and clustergrammer-py libraries. clustergrammer-widget was built using the widget-cookiecutter template ( clustergrammer-widget can be installed using pip ( and the source […]

PMCID: 5533729
PMID: 28754956
DOI: 10.1038/s41598-017-06792-x

[…] might also have developed a facultative ectoparasitic foraging strategy consisting of biting fins of large animals, like in some modern fishes with a specialized cutting dentition (i.e., cookiecutter sharks and piranhas; figs  and and ; see supplementary text , part g). butterfly, eagle and devil rays (gymnuridae, myliobatidae and mobulidae, respectively), whale sharks […]

PMCID: 4835728
PMID: 27089831
DOI: 10.1038/srep24501

[…] using “trim galore!” software ( with default parameters. we then cleaned out reads containing 23-mer illumina-specific primers using cookiecutter (, the cleaned reads from the microdissected chromosomes were mapped to the three assembled asian arowana genomes (golden, red and green) […]

PMCID: 4833346
PMID: 27082250
DOI: 10.1371/journal.pgen.1005954

[…] as well as the repeats present in repbase []., we used the jellyfish software [] for computing 23-mer frequencies and choosing a subset of 23-mers with coverage greater than 1,000. we used the cookiecutter package [] for extraction of raw reads containing subset of 23-mers with coverage greater than 1000. the selected reads were used to manually assemble tandem repeat monomer consensus […]

Cookiecutter institution(s)
Bioinformatics Institute, St. Petersburg, Russia; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Oceanographic Center, Nova Southeastern University Ft Lauderdale, Ft Lauderdale, FL, USA

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